Elevating Public Health Decision Making with R Packages

Kylie Ainslie

Look familiar?

What if there was a better way?

Structure your project as an R package

The Framework

Step 1: Organize
Step 2: Document
Step 3: Share

Let’s travel back in time

June 2021 in the Netherlands

COVID-19 cases decreasing
Vaccination ongoing in adults
Relaxation of control measures

The Challenge

Question: Should the Netherlands extend COVID-19 vaccination to adolescents and children?

Timeline: ~2 weeks

Step #1: Organize

❌ Typical Project

├── analysis.R
├── analysis_v2.R  
├── FINAL_analysis.R
├── analysis_FINAL_v3.R
├── data_raw.csv
├── functions_maybe.R
├── temp_script.R
└── random_test.R

✅ Package Structure

📦 mypackage/
├── R/           # Code
├── data/        # Data  
├── man/         # Help files
└── vignettes/   # Analysis

Impact: Organization → Efficiency

🔄 Models rapidly updated as new data became available
⏰ Analysis delivered on time
💉 Directly informed health policy decisions

Step #2: Document

❌ Separate Documents

├── analysis.R
├── methodology.docx
├── code_guide.pdf
├── final_report.pdf
├── final_report_FINAL.pdf
└── README.txt

✅ Integrated Package

📦 mypackage/
├── R/           # Code
├── man/         # Help files
└── vignettes/   # Docs + Reports
    └── analysis.Rmd → 📊 Report.pdf
                     → 🌐 Website

Vignettes = Dual Purpose

graph TD
    A[📖 analysis.Rmd] --> B[📋 Documentation<br/>for developers]
    A --> C[📊 Deliverable<br/>for clients]
    B --> D[pkgdown website]
    C --> E[PDF report]